Header logo is ps

11 results (View BibTeX file of all listed publications)

2008

Thumb xl jnm
A non-parametric Bayesian alternative to spike sorting

Wood, F., Black, M. J.

J. Neuroscience Methods, 173(1):1–12, August 2008 (article)

Abstract
The analysis of extra-cellular neural recordings typically begins with careful spike sorting and all analysis of the data then rests on the correctness of the resulting spike trains. In many situations this is unproblematic as experimental and spike sorting procedures often focus on well isolated units. There is evidence in the literature, however, that errors in spike sorting can occur even with carefully collected and selected data. Additionally, chronically implanted electrodes and arrays with fixed electrodes cannot be easily adjusted to provide well isolated units. In these situations, multiple units may be recorded and the assignment of waveforms to units may be ambiguous. At the same time, analysis of such data may be both scientifically important and clinically relevant. In this paper we address this issue using a novel probabilistic model that accounts for several important sources of uncertainty and error in spike sorting. In lieu of sorting neural data to produce a single best spike train, we estimate a probabilistic model of spike trains given the observed data. We show how such a distribution over spike sortings can support standard neuroscientific questions while providing a representation of uncertainty in the analysis. As a representative illustration of the approach, we analyzed primary motor cortical tuning with respect to hand movement in data recorded with a chronic multi-electrode array in non-human primates.We found that the probabilistic analysis generally agrees with human sorters but suggests the presence of tuned units not detected by humans.

pdf preprint pdf from publisher PubMed [BibTex]

2008

Wood, F., Black, M. J. A non-parametric Bayesian alternative to spike sorting J. Neuroscience Methods, 173(1):1–12, August 2008 (article)

pdf preprint pdf from publisher PubMed [BibTex]

Thumb xl pointclickimagesmall2
Neural control of computer cursor velocity by decoding motor cortical spiking activity in humans with tetraplegia

(J. Neural Engineering Highlights of 2008 Collection)

Kim, S., Simeral, J., Hochberg, L., Donoghue, J. P., Black, M. J.

J. Neural Engineering, 5, pages: 455–476, 2008 (article)

Abstract
Computer-mediated connections between human motor cortical neurons and assistive devices promise to improve or restore lost function in people with paralysis. Recently, a pilot clinical study of an intracortical neural interface system demonstrated that a tetraplegic human was able to obtain continuous two-dimensional control of a computer cursor using neural activity recorded from his motor cortex. This control, however, was not sufficiently accurate for reliable use in many common computer control tasks. Here, we studied several central design choices for such a system including the kinematic representation for cursor movement, the decoding method that translates neuronal ensemble spiking activity into a control signal and the cursor control task used during training for optimizing the parameters of the decoding method. In two tetraplegic participants, we found that controlling a cursor’s velocity resulted in more accurate closed-loop control than controlling its position directly and that cursor velocity control was achieved more rapidly than position control. Control quality was further improved over conventional linear filters by using a probabilistic method, the Kalman filter, to decode human motor cortical activity. Performance assessment based on standard metrics used for the evaluation of a wide range of pointing devices demonstrated significantly improved cursor control with velocity rather than position decoding.

pdf preprint pdf from publisher [BibTex]

Kim, S., Simeral, J., Hochberg, L., Donoghue, J. P., Black, M. J. Neural control of computer cursor velocity by decoding motor cortical spiking activity in humans with tetraplegia J. Neural Engineering, 5, pages: 455–476, 2008 (article)

pdf preprint pdf from publisher [BibTex]

Thumb xl jmiv08brownian
Brownian Warps for Non-Rigid Registration

Mads Nielsen, Peter Johansen, Andrew Jackson, Benny Lautrup, Soren Hauberg

Journal of Mathematical Imaging and Vision, 31, pages: 221-231, Springer Netherlands, 2008 (article)

Publishers site PDF [BibTex]

Mads Nielsen, Peter Johansen, Andrew Jackson, Benny Lautrup, Soren Hauberg Brownian Warps for Non-Rigid Registration Journal of Mathematical Imaging and Vision, 31, pages: 221-231, Springer Netherlands, 2008 (article)

Publishers site PDF [BibTex]

Thumb xl jmiv08theater
An Efficient Algorithm for Modelling Duration in Hidden Markov Models, with a Dramatic Application

Soren Hauberg, Jakob Sloth

Journal of Mathematical Imaging and Vision, 31, pages: 165-170, Springer Netherlands, 2008 (article)

Publishers site Paper site PDF [BibTex]

Soren Hauberg, Jakob Sloth An Efficient Algorithm for Modelling Duration in Hidden Markov Models, with a Dramatic Application Journal of Mathematical Imaging and Vision, 31, pages: 165-170, Springer Netherlands, 2008 (article)

Publishers site Paper site PDF [BibTex]

2004

Thumb xl woodtransbme04
On the variability of manual spike sorting

Wood, F., Black, M. J., Vargas-Irwin, C., Fellows, M., Donoghue, J. P.

IEEE Trans. Biomedical Engineering, 51(6):912-918, June 2004 (article)

pdf pdf from publisher [BibTex]

2004

Wood, F., Black, M. J., Vargas-Irwin, C., Fellows, M., Donoghue, J. P. On the variability of manual spike sorting IEEE Trans. Biomedical Engineering, 51(6):912-918, June 2004 (article)

pdf pdf from publisher [BibTex]

Thumb xl wutransbme04
Modeling and decoding motor cortical activity using a switching Kalman filter

Wu, W., Black, M. J., Mumford, D., Gao, Y., Bienenstock, E., Donoghue, J. P.

IEEE Trans. Biomedical Engineering, 51(6):933-942, June 2004 (article)

Abstract
We present a switching Kalman filter model for the real-time inference of hand kinematics from a population of motor cortical neurons. Firing rates are modeled as a Gaussian mixture where the mean of each Gaussian component is a linear function of hand kinematics. A “hidden state” models the probability of each mixture component and evolves over time in a Markov chain. The model generalizes previous encoding and decoding methods, addresses the non-Gaussian nature of firing rates, and can cope with crudely sorted neural data common in on-line prosthetic applications.

pdf pdf from publisher [BibTex]

Wu, W., Black, M. J., Mumford, D., Gao, Y., Bienenstock, E., Donoghue, J. P. Modeling and decoding motor cortical activity using a switching Kalman filter IEEE Trans. Biomedical Engineering, 51(6):933-942, June 2004 (article)

pdf pdf from publisher [BibTex]

Thumb xl bildschirmfoto 2013 01 15 um 10.17.00
Development of neural motor prostheses for humans

Donoghue, J., Nurmikko, A., Friehs, G., Black, M.

In Advances in Clinical Neurophysiology, (Editors: Hallett, M. and Phillips, L.H. and Schomer, D.L. and Massey, J.M.), Supplements to Clinical Neurophysiology Vol. 57, 2004 (incollection)

pdf [BibTex]

Donoghue, J., Nurmikko, A., Friehs, G., Black, M. Development of neural motor prostheses for humans In Advances in Clinical Neurophysiology, (Editors: Hallett, M. and Phillips, L.H. and Schomer, D.L. and Massey, J.M.), Supplements to Clinical Neurophysiology Vol. 57, 2004 (incollection)

pdf [BibTex]

2002

Thumb xl bildschirmfoto 2013 01 15 um 10.33.56
Bayesian Inference of Visual Motion Boundaries

Fleet, D. J., Black, M. J., Nestares, O.

In Exploring Artificial Intelligence in the New Millennium, pages: 139-174, (Editors: Lakemeyer, G. and Nebel, B.), Morgan Kaufmann Pub., July 2002 (incollection)

Abstract
This chapter addresses an open problem in visual motion analysis, the estimation of image motion in the vicinity of occlusion boundaries. With a Bayesian formulation, local image motion is explained in terms of multiple, competing, nonlinear models, including models for smooth (translational) motion and for motion boundaries. The generative model for motion boundaries explicitly encodes the orientation of the boundary, the velocities on either side, the motion of the occluding edge over time, and the appearance/disappearance of pixels at the boundary. We formulate the posterior probability distribution over the models and model parameters, conditioned on the image sequence. Approximate inference is achieved with a combination of tools: A Bayesian filter provides for online computation; factored sampling allows us to represent multimodal non-Gaussian distributions and to propagate beliefs with nonlinear dynamics from one time to the next; and mixture models are used to simplify the computation of joint prediction distributions in the Bayesian filter. To efficiently represent such a high-dimensional space, we also initialize samples using the responses of a low-level motion-discontinuity detector. The basic formulation and computational model provide a general probabilistic framework for motion estimation with multiple, nonlinear models.

pdf [BibTex]

2002

Fleet, D. J., Black, M. J., Nestares, O. Bayesian Inference of Visual Motion Boundaries In Exploring Artificial Intelligence in the New Millennium, pages: 139-174, (Editors: Lakemeyer, G. and Nebel, B.), Morgan Kaufmann Pub., July 2002 (incollection)

pdf [BibTex]

1996

Thumb xl bildschirmfoto 2012 12 07 um 11.52.07
Estimating optical flow in segmented images using variable-order parametric models with local deformations

Black, M. J., Jepson, A.

IEEE Transactions on Pattern Analysis and Machine Intelligence, 18(10):972-986, October 1996 (article)

Abstract
This paper presents a new model for estimating optical flow based on the motion of planar regions plus local deformations. The approach exploits brightness information to organize and constrain the interpretation of the motion by using segmented regions of piecewise smooth brightness to hypothesize planar regions in the scene. Parametric flow models are estimated in these regions in a two step process which first computes a coarse fit and estimates the appropriate parameterization of the motion of the region (two, six, or eight parameters). The initial fit is refined using a generalization of the standard area-based regression approaches. Since the assumption of planarity is likely to be violated, we allow local deformations from the planar assumption in the same spirit as physically-based approaches which model shape using coarse parametric models plus local deformations. This parametric+deformation model exploits the strong constraints of parametric approaches while retaining the adaptive nature of regularization approaches. Experimental results on a variety of images indicate that the parametric+deformation model produces accurate flow estimates while the incorporation of brightness segmentation provides precise localization of motion boundaries.

pdf pdf from publisher [BibTex]

1996

Black, M. J., Jepson, A. Estimating optical flow in segmented images using variable-order parametric models with local deformations IEEE Transactions on Pattern Analysis and Machine Intelligence, 18(10):972-986, October 1996 (article)

pdf pdf from publisher [BibTex]

Thumb xl bildschirmfoto 2012 12 07 um 11.59.00
On the unification of line processes, outlier rejection, and robust statistics with applications in early vision

Black, M., Rangarajan, A.

International Journal of Computer Vision , 19(1):57-92, July 1996 (article)

Abstract
The modeling of spatial discontinuities for problems such as surface recovery, segmentation, image reconstruction, and optical flow has been intensely studied in computer vision. While “line-process” models of discontinuities have received a great deal of attention, there has been recent interest in the use of robust statistical techniques to account for discontinuities. This paper unifies the two approaches. To achieve this we generalize the notion of a “line process” to that of an analog “outlier process” and show how a problem formulated in terms of outlier processes can be viewed in terms of robust statistics. We also characterize a class of robust statistical problems for which an equivalent outlier-process formulation exists and give a straightforward method for converting a robust estimation problem into an outlier-process formulation. We show how prior assumptions about the spatial structure of outliers can be expressed as constraints on the recovered analog outlier processes and how traditional continuation methods can be extended to the explicit outlier-process formulation. These results indicate that the outlier-process approach provides a general framework which subsumes the traditional line-process approaches as well as a wide class of robust estimation problems. Examples in surface reconstruction, image segmentation, and optical flow are presented to illustrate the use of outlier processes and to show how the relationship between outlier processes and robust statistics can be exploited. An appendix provides a catalog of common robust error norms and their equivalent outlier-process formulations.

pdf pdf from publisher DOI [BibTex]

Thumb xl bildschirmfoto 2012 12 07 um 12.09.01
The robust estimation of multiple motions: Parametric and piecewise-smooth flow fields

Black, M. J., Anandan, P.

Computer Vision and Image Understanding, 63(1):75-104, January 1996 (article)

Abstract
Most approaches for estimating optical flow assume that, within a finite image region, only a single motion is present. This single motion assumption is violated in common situations involving transparency, depth discontinuities, independently moving objects, shadows, and specular reflections. To robustly estimate optical flow, the single motion assumption must be relaxed. This paper presents a framework based on robust estimation that addresses violations of the brightness constancy and spatial smoothness assumptions caused by multiple motions. We show how the robust estimation framework can be applied to standard formulations of the optical flow problem thus reducing their sensitivity to violations of their underlying assumptions. The approach has been applied to three standard techniques for recovering optical flow: area-based regression, correlation, and regularization with motion discontinuities. This paper focuses on the recovery of multiple parametric motion models within a region, as well as the recovery of piecewise-smooth flow fields, and provides examples with natural and synthetic image sequences.

pdf pdf from publisher [BibTex]

Black, M. J., Anandan, P. The robust estimation of multiple motions: Parametric and piecewise-smooth flow fields Computer Vision and Image Understanding, 63(1):75-104, January 1996 (article)

pdf pdf from publisher [BibTex]